Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold6

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 5058
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30


Found at i:4894 original size:18 final size:16

Alignment explanation


    Indices: 4854--4890  Score: 65
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       4844 TTCAGCAACA

                            
       4854 CAGAGTTGTCGTTCGC
          1 CAGAGTTGTCGTTCGC

                            
       4870 CAGAGTTGTCGTTCGC
          1 CAGAGTTGTCGTTCGC

            *    
       4886 GAGAG
          1 CAGAG

       4891 AGTTCTCCTG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   20  1.00

ACGTcount: A:0.16, C:0.22, G:0.35, T:0.27


Consensus pattern (16 bp):   
CAGAGTTGTCGTTCGC

Left flanking sequence: Indices 4354 -- 4853
TTTGTTTTACTGAAGATCCAGTCGATCGACCAGTAGCATAAACTCAGAAGTGGTTTGAAAATAAG
ATAAGCGATGAAATTATATCCCAATAGGGGTATAATCGACCACAAATCCATCTTATCTGTTGAGA
CTCGACCTCGAGGTCAGAAGCCAAGGGACCGAAGGTACCGCTGGGAAGTTTCTTGTTGTTTTTGG
CCATGGTGAATTTCTTACTCAATTCGAAGGGTACGAAATGCGGTATGGAATTTGATGGAGATCCC
AATAGTCGGGAAACCCCATTCTATATAGTGGAACAATATTCAGGGATGGAAGTTGCGTGATCCGA
TCGGATTGGTTGTGTGATCCGGTCGGGTTTACATTCCTGTAACTACCTCATAATTAGATGGCTAC
CGTCTTGGTTGTGTGCGCAACCAGGTATATGGGAGCCAACATTTACTATCTGTGTTGGAAAGACG
CCTGGTTGCTGATTCGACCGGTGGCAGTCGAACGGTTCAGCAACA


Right flanking sequence: Indices 4891 -- 5058
AGTTCTCCTGGGGAGAAGAGGGCTGAGACATAGTAGATGTCGTAAGCGGTTCTTTTCTAATCAAT
TGAGTTACAGTGGTCTTAGGTTCTTACAGGGCAACGTCGGTATCTATACTATGAGTGGGATACTA
AAGTTGCAAAGGGTAAGTTATAAAGATTTCTGTATTGA


Done.